copasi/basico

Issues

• Fluxes Optimization with Evolutionary Algorithms

  #62 opened 2 months ago by V0idLord
  4

• Time series using "Values" has some quirks

  #61 opened 3 months ago by CodeByDrescher
  10

• support for lyapunov exponents

  #58 opened 2 months ago by fbergmann
  1

• Call to `__build_result_from_ts` (et all?) causes ValueError when imported SBML model names species "Time"

  #60 opened 2 months ago by CodeByDrescher
  3

• issue with display names

  #59 opened 4 months ago by fbergmann
  1

• get_task_settings(): subtask settings not read properly for Scan

  #57 opened 6 months ago by pmendes
  9

• issue with set_reaction_mapping() when mappings are mixed to global quantities and values

  #56 opened 6 months ago by pmendes
  5

• Custom time values with get_simulation_results()

  #54 opened 7 months ago by Theo-BRN
  5

• Inconsistency between COPASI UI parameter estimation and basico parameter estimation

  #55 opened 7 months ago by Theo-BRN
  3

• Simultaneous Parameter Estimation

  #50 opened 9 months ago by Theo-BRN
  5

• Multiple fit_items without all having 'affected'

  #51 opened 6 months ago by Theo-BRN
  1

• is it possible to get notes or annotations of reactions and events?

  #53 opened 8 months ago by pmendes
  3

• if expressions returned incorrectly

  #52 opened 8 months ago by pmendes
  1

• Correct display names check

  #47 opened 9 months ago by Theo-BRN
  2

• get_compartments() returns a type incompatible with set_compartments()

  #49 opened 9 months ago by pmendes
  3

• Cannot find pure Python Wheel for python-copasi package from PyPI

  #48 opened 9 months ago by julien-rudmann
  4

• Mapping bug for multiple experiments in parameter estimation

  #45 opened 9 months ago by Theo-BRN
  6

• Clarification around Parameter Estimation Variables

  #46 opened 9 months ago by Theo-BRN
  2

• error exporting sbml with explicit level and version

  #44 opened 10 months ago by pmendes
  1

• problems with get_events(), spurious spaces in trigger expression

  #43 opened 10 months ago by pmendes
  2

• get_task_settings('Cross Section') does not include variable

  #41 opened 10 months ago by pmendes
  8

• problem setting model initial time

  #40 opened 10 months ago by pmendes
  2

• get_task_settings('Sensitivities') does not include Effect, Cause and Secondary cause

  #42 opened 10 months ago by pmendes
  3

• Error running parameter estimation task

  #39 opened a year ago by lilijap
  5

• installing basico 0.53 on remote ubuntu server via workflow

  #38 opened a year ago by lilijap
  5

• JOSS Review: Error in Working_with_Annotations ipynb

  #34 opened a year ago by ayush9pandey
  2

• JOSS Review: No output file defined in stochastic simulation

  #35 opened a year ago by ayush9pandey
  3

• JOSS Review: Errros in Working_with_ipyparallel

  #36 opened a year ago by ayush9pandey
  2

• JOSS Review: Errors with `pytest`

  #37 opened a year ago by ayush9pandey
  3

• BASICO missing binding for Hybrid Runge Kutta method

  #33 opened 2 years ago by CodeByDrescher
  1

• does basico use threading?

  #32 opened 2 years ago by syedzayyan
  1

• Conditional Stochastic Events

  #30 opened 2 years ago by fabriciocravo
  7

• Progress Report

  #25 opened 2 years ago by fbergmann
  1

• setting a function that requires modifiers, should map them if specified

  #29 opened 2 years ago by fbergmann
  2

• set_species failing to set initial concentration

  #28 opened 2 years ago by pmendes
  3

• How to set mass-action rate constant for a reaction?

  #27 opened 2 years ago by stbachinger
  2

• should `get_simulation_results` update parameters?

  #26 opened 2 years ago by fbergmann
  1

• Names appear different in exp_data and sim_data dataframes

  #24 opened 2 years ago by DeepaMahm
  3

• Plots of steady-state experiments

  #23 opened 3 years ago by DeepaMahm
  3

• AttributeError: 'CDataObject' object has no attribute 'setDblValue' when running plot_per_dependent_variable()

  #22 opened 3 years ago by nicolas-huber
  3

• Need help with parameter estimation

  #21 opened 3 years ago by hasanbaig
  2

• File reading error in Parameter Estimation Task.

  #20 opened 3 years ago by hasanbaig
  2

• changing transient values

  #19 opened 3 years ago by fbergmann
  1

• Custom selection with parameter does not work

  #18 opened 3 years ago by matthiaskoenig
  4

• Species missing from timecourse result

  #17 opened 3 years ago by matthiaskoenig
  2

• Unexpected "ERROR:root:Error while running the simulation: >EXCEPTION 2022-02-22T11:21:58< CTrajectoryMethod (12): Internal step limit exceeded." when setting large stepsize

  #16 opened 3 years ago by TorkelE
  6

• Retrieving information of <Problem> section in tasks.

  #12 opened 3 years ago by hasanbaig
  5

• Slow ssa simulation of large-ish model

  #15 opened 3 years ago by TorkelE
  2

• Increase step size to avoid "CTrajectoryMethod (12): Internal step limit exceeded." error

  #14 opened 3 years ago by TorkelE
  2

• Running Gillespie simulatons

  #13 opened 3 years ago by TorkelE
  2